Categorically ranking animals for feed efficiency

ABSTRACT

The invention provides methods for managing livestock for breeding or production based on one or more measurements of mitochondrial function. Measurement of mitochondrial function may also be correlated with a calculated or known feed efficiency of livestock animals to yield a predicted feed efficiency for the animal. The invention overcomes deficiencies associated with phenotypic assays for predicted breeding and production value.

This application claims benefit of and priority to U.S. ProvisionalPatent Application 60/756,439, filed Jan. 5, 2006, which is hereinincorporated by reference in its entirety.

The United States Government may own certain rights in the inventionpursuant to USDA CSREES Grant No. 2004-34450-14578.

BACKGROUND OF THE INVENTION

1. Field of the Invention

The present invention relates generally to the field of animal breedingand the production of animal food products. More particularly, itconcerns methods for ranking and selecting animals for feed efficiency.

2. Description of Related Art

Little genetic improvement for meat quality or the efficiency ofproduction has occurred in beef cattle populations in the last 100years, despite development of Selection Index theory over 60 years ago(Hazel, 1943). This is due at least in part to the little informationavailable on which to make selection decisions to improve these traits.It is time consuming, difficult, and costly to obtain carcassinformation in commercial packing plants and to retain the identity ofindividual animals. Thus, little information is available upon which tomake breeding decisions to improve the net efficiency of growth.Considerable efforts have been expended to develop live animalultrasound techniques to provide indirect measures of carcass traits.Due to the importance of these traits and their cost and difficulty ofmeasurement, there is a great need for development of measures forselection of beneficial traits in beef cattle such as diagnostic methodsbased on biochemical and genetic markers. Such techniques could greatlyincrease the productivity of breeding programs and eliminate the needfor costly or ineffective phenotypic selections.

Expected Progeny Differences (EPD), a genetic evaluation tool, havegained increasing use in cattle breeding. Many purebred beef and dairycattle organizations now conduct yearly evaluations that calculate EPDfor a number of cattle weight, growth, and production traits witheconomic importance, including birth weight, weaning weight, ribeyearea, and others. However, an EPD for feed efficiency or a trait that isstrongly correlated with feed efficiency has not yet been developed, inpart because a recognized standard for “efficiency” has been lacking.Efficiency may be defined in a number of ways. Ratios of inputs andoutputs, such as gain to feed (G:F) or feed to gain (F:G), also termedthe “Feed Conversion Ratio” (FCR), have been used. However, as notedbelow, these ratios can confound growth rate, body size, and appetitewith metabolic efficiency.

One promising approach for developing a feed efficiency EPD involvesResidual Feed Intake (RFI), sometimes called net feed intake. RFI isdefined as the difference between an animal's actual feed intake and itsexpected feed requirements for maintenance and growth. Thus, it is thevariation in feed intake between animals that remains after requirementsfor maintenance and growth have been removed. Expected feed intake iscalculated based on the statistical modelY=β ₀+β₁ X1+β₂ X2+ε,

wherein Y is expected feed intake; β₀ is a regression intercept; β₁ isthe partial regression of daily feed intake on average daily gain (ADG);X1 is Average Daily Gain; β₂ is the partial regression of daily intakeon body weight; X2 is body weight; and ε is the random error. The bodyweight of the animal is typically expressed as the midweight during test(sometimes transformed to a “metabolic midweight” by raising themidweight to about the power of 0.75, e.g. kg^(0.75); Crews 2005). TheRFI for an animal is calculated as actual feed intake minus expectedintake (Y). The mean RFI for a tested population is zero. Efficientanimals, with an RFI below zero, have daily feed intakes below whatwould have been predicted given their levels of production or bodyweight.

Importantly for breeding purposes, RFI has been found to exhibitmoderate genetic heritability. However, given the phenotypic way inwhich it is calculated, the underlying biochemical and genetic factorsthat result in a given RFI have been unclear. RFI has typically beencalculated by an expensive and time consuming phenotypic process,wherein cattle are subjected to a feeding regimen, and their individualfeed intake and growth are closely followed, typically over a more than70 day period, for instance, in conjunction with use of a feedmanagement system like the GrowSafe® Feed Intake System (U.S. Pat. No.6,868,804), or other cattle management system (e.g. U.S. Pat. No.6,805,075), in order to obtain data on their feed intake and growth.Significantly, RFI may be used as a selection tool that does notconfound metabolic efficiency with growth rate.

Johnson et al. (2003) and Herd et al. (2003) discussed dietary energyuse research in beef cattle production in general, including the use ofcalculated RFI as an efficiency measurement. Basarab et al. (2003)reported differences in average daily feed intake (ADFI) and G:F (gainto feed ratio) when steers grouped according to their calculated RFIwere compared. Basarab also reported increased fat deposition in steersselected to have high RFI. However, mitochondrial function was notexamined. Nkrumah et al. (2004) reported on the relationship between RFIand other measures of energetic efficiency and growth in cattle.However, no underlying mechanism to account for variations in RFIbetween animals was demonstrated.

Moore et al (2005) found that insulin-like growth factor (IGF) wascorrelated to residual feed intake (genetic correlation of 0.35). Theless efficient cattle had higher IGF levels, as would be expected sincethese cattle consume more feed without increased levels of gain. Use ofthis approach to select or predict cattle for feed efficiency canhowever be influenced by the feeding management scheme of the calf, andis not as highly correlated to RFI as mitochondrial respiration rate.Owens et al. (1996; WO96/35127) also describe selection of livestock(e.g. pigs) based on IGF levels.

Bottje and coworkers (Bottje et al. 2002; Iqbal et al., 2004;Ojano-Dirain et al., 2004; WO03/032234) describe aspects ofmitochondrial function, including level of reactive oxygen speciesproduction, that may be used to select for “feed efficiency” (FE) inbroiler chicks. They reported that activity of mitochondrial complexes Iand II was positively correlated with FE in broiler chicks. That is,high FE birds had higher respiratory chain complex activities than lowerFE birds. However, Bottje and coworkers did not use RFI as a measurementof feed efficiency. Rather, their definition of FE, e.g. as a ratioconsisting of the weight gain of an animal divided by the weight of feedconsumed (G:F), or its inverse (F:G), confounds several underlyingvariables, including growth rate, body size, and appetite, with themetabolic efficiency of feed use, per se.

Bottje and coworkers (e.g. Bottje et al., 2002; Iqbal et al., 2004;Ojano-Dirain et al., 2004) reported increased weight gain for chickensdisplaying high feed efficiency, with no difference in feed intakebetween high and low feed efficient birds, and have also reported thatisolated mitochondria of low feed efficient chickens generated greateramounts of hydrogen peroxide than did mitochondria of high feedefficiency birds. Lutz and Stahly (2003) have also described evidence ofa link between inefficient mitochondrial respiration and decreased G:Fin rats.

Sandelin et al. (2004) reported that activities of respiratory chainComplex I and II were higher in low FE steers than in high FE steers.They also use G:F as their measure of FE. The result in cattleapparently contradicts the work of Bottje et al., above in chickens.Thus, the relationship of mitochondrial function as measured bymitochondrial protein activities, rate of electron flux through theelectron transport chain, and correlation to FE (however defined) inanimals is unclear.

SUMMARY OF THE INVENTION

In one aspect, the invention provides a method for predicting metabolicefficiency in a first livestock animal comprising assaying the functionof mitochondria of the first livestock animal and correlating thefunction with the mitochondrial function and feed efficiency of at leasta second livestock animal to obtain a predicted metabolic efficiency forsaid first livestock animal. In certain embodiments, feed efficiency maybe determined by Residual Feed Intake. In other embodiments, assayingthe function of mitochondria of the first livestock animal comprisesassaying at least one characteristic selected from the group consistingof oxygen consumption rate, Complex I electron transport rate, ComplexII electron transport rate, State 2 respiration rate, State 3respiration rate, Respiratory Control Ratio, and ATP synthesis rate. Themethod may further comprise assaying the function of mitochondria of apopulation of livestock animals and correlating the function of themitochondria of the population with the mitochondrial function and feedefficiency of at least a second head of livestock to obtain predictedfeed efficiencies for the members of said population.

In particular embodiments, a method of the invention may compriseranking members of a population based on predicted feed efficiency. Theranking may be based on predicted Residual Feed Intake. A method of theinvention may also further comprise selecting at least a first head oflivestock from the population based on such a ranking and breeding thehead of livestock with a second head of livestock to obtain a progenyhead of livestock. Selecting the first head of livestock may compriseselecting a head of livestock that exhibits a predicted Residual FeedIntake that is less than the average predicted Residual Feed Intake ofthe members of said population.

In a method of the invention, mitochondrial function may be determinedusing mitochondria isolated from muscle or blood cells and themeasurement of mitochondrial function may be a measurement of ATPsynthesis rate. A method of the invention may also further comprisecalculating the Residual Feed Intake of the first livestock animal, andcorrelating the calculated Residual Feed Intake of the first livestockanimal with a measurement of the mitochondrial function of the firstlivestock animal, and/or with the predicted feed efficiency ranking ofthe first livestock animal. The livestock animal(s) may be bovineanimals, such as Bos taurus or Bos indicus cattle, and may be a head ofbeef or dairy cattle.

In another aspect, the invention provides a method of breeding livestockbased on a desired feed efficiency, comprising the steps of: (a)assaying at least a first candidate head of livestock for mitochondrialfunction; (b) correlating the mitochondrial function with themitochondrial function of at least a second head of livestock having aknown feed efficiency to obtain a predicted feed efficiency for thecandidate head of livestock; (c) selecting a first parent head oflivestock having a desired predicted feed efficiency; and (d) breedingthe first parent head of livestock with a second parent head oflivestock to obtain a progeny head of livestock with an increasedprobability of having a desired feed efficiency relative to a head oflivestock of the same breed as said first parent head of livestock orsaid second parent head of livestock that has not been selected for feedefficiency. The first candidate head of livestock may be a bovineanimal.

In one embodiment, feed efficiency is determined by Residual FeedIntake. In another embodiment, the second parent head of livestock isselected based on mitochondrial function for a desired predicted feedefficiency. In still further embodiments, the second parent head oflivestock is selected by a method comprising the steps of: (a) assayinga population of livestock for mitochondrial function; (b) correlatingthe mitochondrial function with the mitochondrial function of at least asecond head of livestock having a known feed efficiency to obtain apredicted feed efficiency for members of the population; and (c)selecting the second parent head of livestock from the population basedon said predicted feed efficiency. Mitochondrial function may bedetermined, for example, based on at least one characteristic selectedfrom the group consisting of oxygen consumption rate, Complex I electrontransport rate, Complex II electron transport rate, State 2 respirationrate, State 3 respiration rate, Respiratory Control Ratio, and ATPsynthesis rate. The method may further comprise crossing said progenyhead of livestock with a third head of livestock to produce a secondgeneration progeny head of livestock. The improved feed efficiency maybe a reduced Residual Feed Intake. In one embodiment, the first parenthead of livestock is a head of beef cattle.

In yet another aspect, the invention provides a method for estimatingthe breeding value of a head of livestock, comprising assaying themitochondrial function of the head of livestock and correlating themitochondrial function with the mitochondrial function and ExpectedProgeny Difference of at least a second head of livestock to obtain apredicted Expected Progeny Difference for said head of livestock. In oneembodiment, the mitochondrial function is determined based on at leastone characteristic selected from the group consisting of oxygenconsumption rate, Complex I electron transport rate, Complex II electrontransport rate, State 2 respiration rate, State 3 respiration rate,Respiratory Control Ratio, and ATP synthesis rate. In specificembodiments, the head of livestock is a bovine animal, and may be a headof beef or dairy cattle.

DETAILED DESCRIPTION OF THE INVENTION

The inventors have surprisingly found that measurement of themitochondrial function of livestock such as cattle allows ranking bypredicted Residual Feed Intake. In contrast, previous studies of therelationship between mitochondrial function and “feed efficiency” asdefined by ratios of weight-gain (G) and feed-consumption (F), e.g. G:For F:G yielded conflicting results. The techniques of the invention aresignificant in that they allow selection of a livestock animal such as ahead of cattle for breeding or food production purposes based on ameasurement of mitochondrial function. With the increasing costsassociated with animal breeding and artificial insemination, each headof livestock produced represents a substantial investment of time andmoney, and the phenotypic calculation of a RFI value for an animal wouldrequire additional time and cost. Selection based on a physiologic traitsuch as mitochondrial function may thus be employed to provide livestockbreeders and/or producers an additional management tool, yieldingreduced cost and increased production efficiency.

The invention thus provides, in one aspect, a method for improvingefficiencies in livestock production. The invention in particularprovides methods for predicting the ranked growth pattern of livestockanimals by identifying a physiological indicator in the animals thatcorrelates with calculated Residual Feed Intake, a measure of themetabolic feed efficiency of an animal. This allows efficient managementof livestock for breeding and production purposes through screening forthat physiological indicator.

The invention therefore provides methods for the improvement of beefcattle with respect to feed efficiency as measured by Residual FeedIntake (RFI). It was found that a measurement of mitochondrial functioncan be correlated with the calculated RFI of a bovine animal. RFI is arobust measure of metabolic efficiency that does not confoundmeasurement of an animal's metabolic efficiency with growth rate, size,or appetite. Thus, a biochemical assay of mitochondrial function maysubstitute for, or be used in addition to, the costly and time consumingphenotypic calculation of RFI or other methods of determining feedefficiency. This allows development and use of selection tools such asExpected Progeny Differences (EPD) for one or more metabolic efficiencyparameters, including mitochondrial function. Mitochondrial function maybe assayed by measurements of oxygen consumption, ATP synthesis, State 2respiration rate, State 3 respiration rate, and respiratory controlratio (RCR), among others. Measurement of mitochondrial function mayalso be used in conjunction with other known markers, including genetic,phenotypic, and biochemical markers, in order to make management andselection decisions in bovine livestock breeding and productionsettings.

Another aspect of the present invention is an improved method forlivestock selection comprising correlating the phenotypic feedefficiency of an animal with a measurement of the animal's mitochondrialfunction. In one embodiment of the invention, the calculation ofphenotypic feed efficiency may be by phenotypic determination ofresidual feed intake. The residual feed intake (Koch et al., 1963) maybe calculated by methods known in the art, and as described below, forinstance, through use of the GrowSafe™ feed management system. Inanother embodiment, the feed efficiency of the animal is calculatedusing the Cornell Value Discovery System(www.cvds.cals.cornell.edu/cvds/; Fox et al., 2004), or another methodto calculate a feed conversion ratio, although such a ratio may be lessaccurate or statistically robust than a calculated RFI. Feed efficiencyand growth and production data that may be correlated with mitochondrialfunction measurements for selection or breeding purposes can also beobtained by other methods or management systems known in the art (e.g.U.S. Pat. No. 6,805,075). Livestock selection may be for purposes ofbreeding, or for production of food such as beef or dairy products.

In one embodiment, a measurement of the animal's mitochondrial functionmay be made by biochemical testing of the enzymatic function ofmitochondria isolated from muscle cells. In another embodiment, themitochondria may be isolated from blood cells such as lymphocytes. Inaccordance with the invention any assay which sorts and identifiescattle based upon differences in mitochondrial function may be used andis specifically included within the scope of this invention.Non-limiting examples of such assays include oxygen consumption, State 2respiration rate (oxygen consumption in isolated mitochondria in thepresence substrate and absence of ADP), State 3 respiration rate(ADP-stimulated oxygen consumption), State 4 respiration rate (oxygenconsumption by isolated mitochondria in the absence of ADP or anymetabolic poisons or inhibitors), acceptor control ratio (ACR: ratio ofState 3 to State 2 respiration rates), respiratory control ratio (RCR;ratio of State 3 respiration rate to State 4 respiration rate), ADP:O(ratio of added ADP to atomic oxygen consumed during oxidativephosphorylation of ADP to ATP), and hydrogen peroxide (H₂O₂) production.

One aspect of the present invention comprises a method for predictingthe RFI of an animal based on a measurement of its mitochondrialfunction, prior to, or in the absence of, a calculation of itsphenotypic RFI. Thus, a measurement of mitochondrial function maysubstitute for a calculation of phenotypic feed efficiency, such as bycalculation of RFI, for the purpose of making selection decisions.

Another aspect of the present invention comprises a method for using ameasurement of mitochondrial function in conjunction with the use of oneor more other selection or management tools. These tools may includephenotypic evaluations of animal growth, feed intake, and feedefficiency, including calculation of RFI; ultrasound measurements suchas fat depth measurements, marbling scores, and ribeye area; weight gainand other measurements. These tools may also include other biochemicalor genetic tests to characterize an animal's efficiency of growth.

The use of biochemical assays to identify livestock displaying improvedfeed efficiency will find use in breeding or selecting of livestockproduced for slaughter, e.g., for production of meat products, byallowing a reduction in feed use. Costs associated with feeding,including cost of feed and manure and methane production could thus bereduced. Thus, one embodiment of the invention comprises a breedingprogram directed at enhancement of feed efficiency in livestock breeds,especially beef cattle breeds adapted for meat production. Suchtechniques have to date been largely lacking for beef cattle.Enhancement of feed efficiency may be noted by a reduced RFI value. Themethod may also be applied to other bovine animals, including dairycattle. The availability of this additional selection tool forbeneficial livestock traits therefore represents a significant advance.Biochemical assays for mitochondrial function may also be employed inconjunction with other selection tools, including genetic markers suchas for growth traits (e.g. Kneeland et al., 2004). Genetic markers to beemployed may be either nuclear markers or mitochondrial markers.Breeding records may also be employed to correlate mitochondrialfunction with RFI or another measure of feed efficiency, phenotypicevaluation, and other biochemical, physiological, and phenotypic tools,allowing development and use of Expected Progeny Differences (EPD)related to mitochondrial function and/or feed efficiency as a tool forlivestock production and breeding decisions.

As used herein, the term “Residual Feed Intake” (RFI), sometimesreferred to as “net feed efficiency” or “net feed intake”, is thedifference between actual feed intake and that predicted on the basis ofmean requirements for body weight maintenance and level of production.Thus, efficient animals, with an RFI value below zero, have daily feedintakes less than would be predicted given their level of production andbody weight.

Most natural populations of animals are genetically quite different fromthe classical linkage mapping populations. While linkage mappingpopulations are commonly derived from two-generation crosses between twoparents, many natural populations are derived from multi-generationmatings between an assortment of different parents, resulting in amassive reshuffling of genes. Individuals in such populations carry acomplex mosaic of genes, derived from a number of different founders ofthe population. Gene frequencies in the population as a whole may bemodified by a natural or artificial selection, or by genetic drift(e.g., chance) in small populations. Given such a complex populationwith superior average expression of a trait, a breeder might wish to (1)maintain or improve the expression of the trait of interest, whilemaintaining desirable levels of other traits; and (2) maintainsufficient genetic diversity that rare desirable alleles influencing thetrait(s) of interest are not lost before their frequency can beincreased by selection.

Genetic and biochemical assays may find particular utility inmaintaining sufficient diversity in a population while maintainingfavorable alleles. For example, one might select a fraction of thepopulation based on favorable phenotype (perhaps for several traits—onemight readily employ index selection), then apply genetic or biochemicalassays as described herein to this fraction and keep a subset whichrepresent much of the allelic diversity within the population.Strategies for extracting a maximum of desirable phenotypic variationfrom complex populations remain an important area of breeding strategy.An integrated approach, merging classical phenotypic selection withbiochemical and/or genetic marker-based analysis, may aid in identifyingvaluable genotypes from heterogeneous populations.

The techniques of the invention may be applied, in certain embodiments,in connection with any livestock animal. As used herein, “livestock”generally to animals raised primarily for food. For example, suchanimals include, but are not limited to, cattle (bovine), sheep (ovine),and pigs (porcine or swine) and the like. In a specific aspect of theinvention, the livestock may be a defined as not a poultry animal. Asused herein, the term “cow” or “cattle” is used generally to refer to ananimal of bovine origin of any age. Interchangeable terms include“bovine”, “calf”, “steer”, “bull”, “heifer” and the like. As usedherein, the term “pig” is used generally to refer to an animal ofporcine origin of any age.

The techniques of the present invention may potentially be used with anybovine, including Bos taurus and Bos indicus cattle. In particularembodiments of the invention, the techniques described herein arespecifically applied for selection of beef cattle, as the methodsdescribed herein will find utility in maximizing production of animalproducts, such as meat. As used herein, the term “beef cattle” refers tocattle grown or bred for production of meat or other non-dairy animalproducts. Therefore, a “head of beef cattle” refers to at least a firstbovine animal grown or bred for production of meat or other non-dairyanimal products. Examples of breeds of cattle that may be used with theinvention include, but are not limited to, Africander, Albères,Alentejana, American, American White Park, Amerifax, Amrit Mahal,Anatolian Black, Andalusian Black, Andalusian Grey, Angeln, Angus,Ankole, Ankole-Watusi, Argentine Criollo, Asturian Mountain, AsturianValley, Australian Braford, Australian Lowline, Bachaur, Baladi, Barka,Barzona, Bazadais, Beefalo, Beefmaker, Beefmaster, Belarus Red, BelgianBlue, Belgian Red, Belmont Adaptaur, Belmont Red, Belted Galloway,Bengali, Berrendas, Bhagnari, Blanco Orejinegro, Blonde d'Aquitaine,Bonsmara, Boran, Braford, Brahman, Brahmousin, Brangus, Braunvieh,British White, Busa, Cachena, Canary Island, Canchim, Carinthian Blond,Caucasian, Channi, Charbray, Charolais, Chianina, Cholistani, Corriente,Costeño con Cuernos, Dajal, Damietta, Dangi, Deoni, Devon, Dexter,Dhanni, Dølafe, Droughtmaster, Dulong, East Anatolian Red, EnderbyIsland, English Longhorn, Evolène, Fighting Bull, FloridaCracker/Pineywoods, Galician Blond, Galloway, Gaolao, Gascon, Gelbray,Gelbvieh, German Angus, German Red Pied, Gir, Glan, Greek Shorthorn,Guzerat, Hallikar, Hariana, Hays Converter, Hereford, Herens, Highland,Hinterwald, Holando-Argentino, Horro, Hungarian Grey, Indo-Brazilian,Irish Moiled, Israeli Red, Jamaica Black, Jamaica Red, Jaulan, Kangayam,Kankrej, Kazakh, Kenwariya, Kerry, Kherigarh, Khillari, Krishna Valley,Kurdi, Kuri, Limousin, Lincoln Red, Lohani, Luing, Maine Anjou, Malvi,Mandalong, Marchigiana, Masai, Mashona, Mewati, Mirandesa, Mongolian,Morucha, Murboden, Murray Grey, Nagori, N'dama, Nelore, Nguni, Nimari,Ongole, Orma Boran, Oropa, Parthenais, Philippine Native, Polish Red,Polled Hereford, Ponwar, Piedmontese, Pinzgauer, Qinchuan, Rätien Gray,Rath, Rathi, Red Angus, Red Brangus, Red Poll, Retinta, Rojhan,Romagnola, Romosinuano, RX3, Sahiwal, Salers, Salorn, Sanhe, Santa Cruz,Santa Gertrudis, San Martinero, Sarabi, Senepol, Sharabi, Shorthorn,Simbrah, Simmental, Siri, Slovenian Cika, South Devon, Sussex, SwedishRed Polled, Tarentaise, Telemark, Texas Longhorn, Texon, Tharparkar,Tswana, Tuli, Ukrainian Beef, Ukrainian Grey, Ukrainian Whitehead,Umblachery, Ural Black Pied, Väneko, Vestland Red Polled, Vosges, Wagyu,Welsh Black, White Cáceres, White Park, Xinjiang Brown and Yanbiancattle breeds, as well as animals bred therefrom and related thereto.

The techniques of the present invention may also be applied to dairycattle breeds such as, among others, Ayrshire, Brown Swiss, Canadienne,Dutch Belted, Guernsey, Holstein, Jersey, Kerry, Milking Devon, MilkingShorthorn, and Norwegian Red as well as animals bred therefrom andrelated thereto.

Food production using the methods of the present invention includes beefproduction, production of beef byproducts, and production of one or moredairy products, such as milk and products derived therefrom. Productionof inedible beef byproducts may also utilize the methods of the presentinvention. Selection of one or more head of cattle based on the methodsof the present invention for breeding or production purposes may beperformed on one or more calves, heifers, bull-calves, steers, cows, orbulls.

Techniques for nucleic acid detection may find use in certainembodiments of the invention. For example, such techniques may find usein scoring individuals for certain genotypes, such as the development ofnovel genetic markers linked to mitochondrial respiration activities(phenotypes). Such nucleic acid detection techniques may includenucleotide hybridization or PCR™ assays to identify specific markersequences, and to follow their segregation during a program of bovinebreeding and selection.

EXAMPLES

The following examples are included to demonstrate preferred embodimentsof the invention. It should be appreciated by those of skill in the artthat the techniques disclosed in the examples which follow representtechniques discovered by the inventor to function well in the practiceof the invention, and thus can be considered to constitute preferredmodes for its practice. However, those of skill in the art should, inlight of the present disclosure, appreciate that many changes can bemade in the specific embodiments which are disclosed and still obtain alike or similar result without departing from the spirit and scope ofthe invention.

Example 1 Animal Management and Statistical Analyses

Forty Angus steers (average initial BW=325.4±23.7 kg) were used toselect high and low residual feed intake (RFI) animals. Steers wereobtained from a single herd enrolled in the MFA Health Track BeefAlliance, were all of the same sire, and had been previously vaccinatedand preconditioned for 45 d before arrival at the University of MissouriBeef Research Farm. The animals were tagged with electronic ID tags(Allflex USA, Inc.; Dallas Ft. Worth Airport, Tex.) upon receipt, formeasurement of individual feed intake with the GrowSafe feed intakesystem (GrowSafe Systems Ltd.; Airdrie, AB Canada; U.S. Pat. No.6,868,804). Steers were placed on a receiving diet for 14 d to allow foracclimation to the feeding system. Following the acclimation period,steers were fed Trendsetter SLR (MFA, Inc.; Columbia, Mo.) at a rate of25% Trendsetter SLR and 75% whole corn until they reached 454 kg. At 454kg, the diet was switched to 12.5% Trendsetter SLR and 87.5% whole cornfor the remainder of the experiment. All steers had ad libitum access toboth feed and water. Steers were weighed every 21 d and RFI values werecalculated for each 21 d period and the entire feeding period. Expectedfeed intake was calculated by regressing actual intake against ADG andmetabolic mid weight (Basarab et al., 2003).

The RFI value for each animal was calculated as the difference betweenthe actual and expected intake. Nine low and eight high RFI steers wereselected based on their RFI values and were used for the study ofmitochondrial respiration. Calculated RFI is shown in Table 1, alongwith other production parameters. These 17 steers were transported tothe University of Missouri Abattoir where the animals were sacrificed toobtain tissue from the LM (longissimus lumborum muscles) formitochondrial isolation. Hot carcass weights were documented for eachanimal and the carcasses were chilled for a 24 hr period at 5° C.Following a 24 hr chill, LM area of each carcass was measured to thenearest 0.01 cm². Subcutaneous fat thickness at the 12^(th) rib wasdetermined using a USDA preliminary yield grade ruler (USDA, 1997) at ananatomical location perpendicular to the vertebral column and ¾ thedistance, caudal the LM. To determine preliminary yield grades, the fatmeasurements were then adjusted, correcting for any atypical fatdistribution.

The data were analyzed using the General Linear Model Procedure (SASInst., Inc.; Cary, N.C.) as a completely randomized design. An alphalevel of 0.05 was used for the determination of statisticalsignificance. The performance of high and low RFI steers is shown inTable 1.

TABLE 1 Performance of steers with high or low residual feed intake(RFI) Variable Low RFI (n = 9) High RFI (n = 8) Initial BW, kg 332.78 ±6.75  330.17 ± 7.16  Final BW, kg 566.77 ± 10.00  563.07 ± 10.61  ADG,kg/d 1.48 ± 0.05 1.47 ± 0.05 G:F  0.20 ± 0.01^(a)  0.16 ± 0.01^(b) ADFI,kg/d  7.40 ± 1.98^(b)  8.94 ± 2.10^(a) Residual feed intake −0.83 ±0.09^(b)  0.78 ± 0.10^(a) HCW, kg 352.17 ± 9.58  367.61 ± 10.16 Longissimus dorsi area, cm² 76.7 ± 1.15 79.74 ± 1.22  Fat thickness overthe 12^(th) rib, cm 2.16 ± 0.15 1.92 ± 0.15 USDA yield grade 4.27 ± 0.204.00 ± 0.22 ^(a,b)Means within a row lacking a common superscript differ(P < 0.001). BW: Body weight HCW: Hot carcass weight ADG: Average dailygain G:F: Gain to feed ratio

A further analysis was also made, comparing the performance of steerswith high, mid or low residual feed intake. The results are presented inTable 2 below.

TABLE 2 Additional analysis of performance of steers with high, mid orlow residual feed intake (RFI) Variable Low RFI Mid RFI High RFI SEMInitial BW, kg 282.20 312.05 293.56 16.23 Final BW, kg 514.47 540.07518.26 21.77 ADG, kg/d 1.39 1.36 1.34 0.06 G:F 0.17^(a) 0.14^(b)0.13^(b) 0.004 ADFI, kg/d 8.39^(b) 9.89^(a) 10.82^(a) 0.38 Residual feedintake −1.24^(c) 0.24^(b) 1.35^(a) 0.19 HCW, kg 316.67 331.52 328.8613.30 Longissimus dorsi area, 74.09 80.65 78.17 2.61 cm² Fat thicknessover the 12^(th) 1.32 1.43 1.27 0.24 rib, cm USDA yield grade 3.00 2.833.17 0.25 ^(a,b)Means within a row lacking a common superscript differ(P < 0.01). BW: Body weight HCW: Hot carcass weight ADG: Average dailygain G:F: Gain to feed ratio

G:F and ADFI were both significantly lower and greater respectively forthe high RFI steers, which consumed 1.54 kg more feed per day than thelow RFI steers. Carcass composition as assessed by LM (Longissimuslumborum muscle) area, fat thickness over 12^(th) rib, HCW, and USDAyield grade were not significantly different between the high and lowRFI groups.

Example 2 Isolation of Mitochondria from Skeletal Muscle

All steps were performed at 0-4° C. unless otherwise stated. Between4-10 g of LM tissue was taken with a scalpel, weighed, added to acentrifuge tube containing 30 ml of ice cold medium 1 (100 mM sucrose;10 mM EDTA; 100 mM tris-HCl; 46 mM KCl; pH 7.4) and placed on ice. 1 mLNagarase solution (8 mg Nagarase/1 mL distilled water) was added and thecontents of the tube was placed on a shaker/mixer. The tube wasincubated at room temperature (25° C.) for 5 minutes with intermittentmixing throughout the incubation period. The contents of the centrifugetube were then poured into a Potter-Elvenhjem vessel with Teflon pestleof 0.16 mm clearance for homogenization. Seven complete passes were madewith the Teflon pestle. The contents were then poured back into thecentrifuge tubes and placed on ice for 5-minutes with intervalshaking/mixing of the tubes. The resulting homogenate was centrifuged at1,000-×g for 10 minutes. The supernatant was poured into a high-speedcentrifuge tube and the pellet was discarded. The supernatant wascentrifuged at 10,000-×g for 15 minutes, and supernatant was discarded.The resulting mitochondrial pellets were resuspended and washed in 10 mLof Medium 1 with 1 mL BSA (5 mg BSA/1 mL in distilled water). The pelletwas then centrifuged at 10,000×g for 15 minutes to collect the pellets,and supernatant was discarded. The resulting pellets were resuspended in20 mL of incubation medium 2 (230 mM mannitol; 70 mM sucrose; 20 mMtris-HCl; 5 mM KH2PO4; pH 7.4) and centrifuged at 8,000-×g for 15minutes. The resulting pellets were resuspended in 2.0 mL of incubationmedium 2 and placed on ice for subsequent studies. Mitochondrial proteinwas determined by the Coomassie Plus protein assay kit (PierceBiotechnology, Inc.; Rockford, Ill.). Measurements of mitochondrialfunction in high or low RFI steers is shown in Table 3.

Example 3 Mitochondrial Oxygen Consumption Measurement

Oxygen consumption (expressed in nmol/min/mg mitochondrial protein) wasmeasured with a with a Clark-type oxygen probe, e.g. YSI model 5300biological oxygen monitor (YSI, Inc.; Yellow Spring, Ohio), induplicate. All measurements were completed within 3 hours of isolation.Measurements were performed in a 30° C. circulating water bath.

3 mL of air-equilibrated RCR buffer, (220 mM d-mannitol; 70 mM sucrose;2 mM HEPES; 3 mM KH₂PO₄; pH 7.0) is placed in the prepared standardprobe sample chamber of the oxygen monitor. All air is removed from thesample chamber, and the monitor is calibrated to 21%. Aliquots (0.3 mL)of the muscle mitochondrial mixture are added via syringe to thereaction vessel containing 3 mL of RCR reaction buffer. Themitochondrial solution was allowed to equilibrate, substrate was thenadded to the chamber: either 100 μL of a 0.5M glutamate solution and 10μL of a 0.5M malate solution (for stimulation of complex I respiration);or 100 μL of a 0.5 M succinate solution (for stimulation of complex IIrespiration).

The oxygen consumption curve was allowed to decrease in a linear fashion(unprimed or basal rate (state 2 respiration)). Then 10 μL of ADP (50 mMsolution) was added and the reaction allowed to run until all the ADPwas utilized (state 3 respiration). Once ADP becomes limiting, the curvelevels out to its unprimed or basal rate. The slope was allowed toreturn (state 4 respiration) and then another 10 μL of ADP was added toachieve state 3 respiration. Steps were repeated until all oxygen wasconsumed. ADP:O ratio was calculated according to the methods ofEastbrook (1967).

Example 4 Lymphocyte Isolation

Blood was collected in a CPT Vacutainer. The tube was inverted 8-10times to mix anticoagulant, and stored upright at room temperature untilcentrifugation (within 2 hours). The tube was inverted several timesbefore centrifuging at 1500-1800 RCF in a swinging bucket centrifuge for20-30 minutes at 18-25° C. Half of the plasma was removed and discarded.Cells were suspended by pipetting and cells/plasma were collected into a15 mL centrifuge tube. Alternatively the tube can be gently inverted5-10 times and stored until collection up to 24 hours later.

Phosphate Buffered Saline (PBS; (0.137M NaCl, 0.0027M KCl, 0.0022MKH₂PO₄, 0.0097M Na₂HPO₄ Anhydrous, pH 7.4)) was added to bring thevolume to 13 mL and the tube is mixed by inverting 5 times. The tube wascentrifuged for 15 minutes at 300 RCF, and supernatant was removed.Cells were resuspended in a 10 ml volume of PBS, mixed by inverting 5times, centrifuged for 10 minutes at 300 RCF, and supernatant wasremoved.

Cells were suspended in 2 mL of storage medium (50% MEM, 40% Fetalbovine serum, 10% DMSO) and stored at −80° C. Alternatively, one maysuspend fresh cells in 5 mL MEM (Modified Eagle's Medium) formeasurement of ATP synthesis.

Example 5 Lymphocyte Isolation and ATP Determination

A. Cell Incubation and Number

Frozen cells were resuspended in 5 mL of MEM, pelleted by centrifugingat 2000×g for 10 min, washed twice with 5 mL of sucrose medium (0.25MSucrose; 5 mM Tris; 2 mM; pH 7.4), centrifuged at 2000×g for 10 min, andresuspended in 2.5 mL incubation buffer (150 mM KCl; 25 mM Tris; 2 mMEDTA; 10 mM KH₂PO₄; pH 7.4 with 0.1% BSA; 1 mM ADP; and 80 μg/mLdigitonin) and divided into 5 500 μL aliquots, and resuspended bypipetting or vortexing. One aliquot was reserved to determine cellnumber. Cells were then incubated with 10 μL of substrate (100 mMGlutamate or 100 mM Succinate) at 37° C. for 0, 5, 15, and 30 minutes.17.5 uL 1.6M perchloric acid was added to stop the reaction and cellswere centrifuged at 13,000×g for 10 minutes to pellet cell debris.Supernatant was removed to a new tube for the determination of ATPconcentration, and 25 uL 1.6M NaOH was added to adjust pH to ˜7.8.

To determine cell number, 50 μL of cells was added to 50 μL of PBS. 50μL of 0.4% trypan blue was added, cells were incubated for 5 min. Bluecells were counted with a hemocytometer to determine cell number.

B. ATP Concentration (Using Sigma FL-AA Kit)

ATP assay mix was dissolved in 5 mL sterile water, and incubated on ice1 hr. ATP dilution buffer was dissolved in 50 mL sterile water. ATPassay mix was diluted 1:25 with ATP dilution buffer (100 μL in 2.5 mLbuffer), a 100 μl sample was added to well and then 100 μl ATP assayreagent was added. The plate was then sealed and read in luminometer.

Example 6 Analysis of Hydrogen Peroxide Production in RespiringMitochondria

The production of hydrogen peroxide by mitochondria isolated from steersselected to have a high or low RFI was measured using the procedures ofBottje et al. (2002) with modifications. Hydrogen peroxide was measuredusing the dichloroflourescin diacetate probe (Molecular Probes, Inc.;Eugene, Oreg.) in a 96-well plate fluorimeter (Fluoroskan Ascent; ThermoElectron Corporation, Vantaa, Finland). Mitochondria (0.05 to 0.1 mgprotein) were incubated with 52 μM dichloroflourescin diacetate, 64 μLbuffer (145 mM KCl, 30 mM HEPES, 15 mM KH₂PO₄, 3 mM MgCl, 0.1 mM EGTA,pH 7.4), 10 U superoxide dismutase, and either 10 mM glutamate orsuccinate. Samples were incubated at 37° C. for 40 min with fluorescencemeasured every 5 min. Hydrogen peroxide production is calculated from astandard curve and is expressed as nmol H₂O₂ generated min⁻¹ mg ofmitochondrial proteins⁻¹. Hydrogen peroxide production is indicative ofelectron leakage in respiring mitochondria.

TABLE 3 Respiratory function of skeletal muscle mitochondria from steerswith high or low residual feed intake (RFI) Glutamate SuccinateVariable¹ Low RFI (n = 9) High RFI (n = 8) Low RFI (n = 9) High RFI (n =8) State 2 respiration  98.00 ± 10.19^(a) 62.78 ± 9.53^(b) 109.45 ±8.05^(a ) 77.35 ± 8.05^(b) State 3 respiration 275.17 ± 27.77^(a) 182.87± 27.77^(b) 482.90 ± 44.83^(a) 344.33 ± 44.83^(b) State 4 respiration84.68 ± 4.97  79.72 ± 4.97  155.47 ± 16.51  133.67 ± 16.51  ACR 3.11 ±0.20 2.68 ± 0.22 4.62 ± 0.28 3.93 ± 0.28 RCR  3.09 ± 0.25^(a)  2.28 ±0.25^(b)  3.84 ± 0.19^(a)  2.50 ± 0.19^(b) ADP:O 2.02 ± 0.11 1.80 ± 0.111.92 ± 0.06 1.76 ± 0.06 H₂O₂ production  4.16 ± 0.43^(a)  2.77 ±0.46^(b) 13.95 ± 1.95^(a)  6.20 ± 2.25^(b) State 2 respiration/ 22.46 ±2.37  20.42 ± 2.37  11.17 ± 2.63  9.42 ± 2.81 H₂O₂ Production ¹ACR =acceptor control ratio (State 3/State 2), RCR = respiratory controlratio (State 3/State 4), ADP:O = adenosine diphosphate to oxygenconsumption ratio, H₂O₂ production is presented as nmol H₂O₂ producedmin.⁻¹ mg mitochondrial protein⁻¹, State 2, 3 and 4 respiration data arepresented as nmol O₂ consumed min.⁻¹ mg mitochondrial protein⁻¹.^(a,b)Means within a row lacking a common superscript differ (P < 0.05).

An analysis was also made comparing respiratory function of skeletalmuscle mitochondria from steers with high, mid or low residual feedintake. The results are presented in Table 4 below.

TABLE 4 Respiratory function of skeletal muscle mitochondria from steerswith high, mid or low residual feed intake (RFI) Glutamate Succinate LowMid High Low Mid High Variable¹ RFI RFI RFI SEM RFI RFI RFI SEM State 2respiration 65.05^(a) 46.73^(b) 37.84^(b) 6.56 95.67^(a) 74.62^(b)56.36^(c) 5.86 State 3 respiration 165.17^(a) 138.29^(a,b) 116.11^(b)13.46 265.78^(a) 214.48^(a) 129.42^(b) 34.57 State 4 respiration 68.6768.97 69.15 9.81 86.40 84.96 69.76 7.13 ACR 3.08 3.22 3.16 0.29 2.702.71 2.41 0.23 RCR 2.80^(a) 2.46^(a) 1.72^(b) 0.16 2.77^(a) 2.44^(a)2.03^(b) 0.18 ADP:O 2.52 2.35 2.26 0.17 1.94 1.86 2.00 0.12 H₂O₂production 0.39^(a) 0.19^(b) 0.13^(b) 0.08 7.90^(a) 3.40^(b) 1.75^(b)0.94 State 2 respiration/ 246.33 294.84 217.85 20.29 19.20 13.14 20.868.85 H₂O₂ production ¹ACR = acceptor control ratio (State 3/State 2),RCR = respiratory control ratio (State 3/ State 4), ADP:O = adenosinediphosphate to oxygen consumption ratio, H₂O₂ production is presented asnmol H₂O₂ produced min.⁻¹ mg mitochondrial protein⁻¹, State 2, 3 and 4respiration data are presented as nmol O₂ consumed min.⁻¹ mgmitochondrial protein⁻¹. ^(a,b)Means within a row lacking a commonsuperscript differ (P < 0.05).

As seen in the tables above, analysis of respiratory function ofmitochondria isolated from the LM of high and low RFI steers shows that,when mitochondria were provided with either glutamate or succinate,there was no significant difference in ACR or ADP:O ratios among steersgrouped for differing RFI. The respiratory control ratio (RCR) of lowRFI steers was significantly greater than that of high RFI steers. Agreater respiratory control ratio results from a greater degree ofcoupling between respiration and oxidative phosphorylation, and suggestsincreased efficiency of electron transfer. Thus, mitochondria from highRFI animals, with a lower RCR, would be expected to demonstrate moreelectron leak and hence H₂O₂ production than those from low RFI animals.However, mitochondria isolated from high RFI steers producedsignificantly less hydrogen peroxide, indicative of electron leak, thanthose from low RFI steers. Because electron leak is a function ofrespiration rate (Chance et al, 1979), H₂O₂ production was alsoexpressed as a ratio to State 2 respiration rate. No difference betweenhigh and low RFI steers in the amount of electron leak was observed whenH₂O₂ production was expressed as a ratio to State 2 respiration rate.Thus, mitochondrial function as measured by H₂O₂ production was notimpaired in high RFI steers. Instead the flux of electrons through theelectron transport chain appears to be impaired

Example 7 Measurement of Plasma Glucose and Insulin Concentration

Blood was collected by jugular venipuncture one week before slaughterinto vacutainers containing EDTA as an anticoagulant (Becton, Dickinsonand Company; Franklin Lakes, N.J.). Samples were collected in themorning before the animal's first major feeding event. The blood sampleswere centrifuged at 2,200×g for 15 min, the plasma was decanted andfrozen at −20° C. until further analysis.

Plasma glucose was determined using a colorimetric glucose oxidase kit(Thermo Electron Corporation; Louisville, Colo.) according to themanufacture's instructions. Plasma concentrations of insulin werequantified using a specific, double-antibody, equilibriumradioimmunoassay as described by Elsasser et al. (1986) with somemodifications. Preparation of bovine insulin (Sigma-Aldrich Co.; StLouis, Mo.) for iodination and for standard curve material was via themethod of Sodoyez et al. (1975) for preparation of zinc free insulin.Ten μg of zinc free bovine insulin was then solubilized in 50 μl H₂O,combined with 500 μCi ¹²⁵I—Na, and incubated in the presence of 100 μgof iodogen (Pierce Biotechnology, Inc., Rockford, Ill.) for 6 min withgentle mixing.

Recovery of the mono-iodinated form of ¹²⁵I-bovine insulin was achievedby differential elution from a 10 ml Sep-Pak C18 Cartridge as previouslydescribed by Deleo (1994) as follows. The Sep-Pak C18 Cartridge wasinitially washed with 10 ml of 50% (v/v) acetonitrile containing 50 mMtriethylamine solution (pH adjusted to pH 3 with phosphoric acid),followed by 10 ml of deionized H₂O before addition of the iodinationmixture. The cartridge was then washed sequentially with: a) 5 ml of 0.4M phosphate buffer pH 7.4, b) 10 ml of 29% (v/v) acetonitrile containing50 mM triethylamine, c) 5 ml of 10% (v/v) acetonitrile containing 0.2 Mammonium acetate, pH 5.5, and finally d) 5 ml of 50% (v/v) acetonitrilecontaining 0.2 M ammonium acetate, pH 5.5. This final fraction wascollected and diluted to 25,000 cpm per 100 μl of assay buffer (0.1%gelatin, 0.01 M EDTA, 0.9% NaCL, 0.01 M PO₄, 0.01% sodium azide, 0.1%Tween-20, pH 7.1). Guinea pig anti-bovine insulin antisera (Elsasser etal., 1986) was diluted to a final tube dilution of 1:167,000 in assaybuffer. Standard concentrations of zinc free bovine insulin (0.064 to 40ng/tube) and increasing volumes of a bovine plasma pool (25 to 300 μl)were added to assay tubes in quadruplicate and the total volume balancedto 300 μl per tube with assay buffer.

All plasma samples (100 μl aliquots) to be analyzed were assayed intriplicate. All components were then incubated at 4° C. for 24 h. Theantigen-antibody complex was then precipitated following a 15-min, 22°C. incubation with 100 μL of a precipitated sheep-anti-guinea pig secondantibody. The second antibody complex was then precipitated bycentrifugation at 3,000 g for 30 min and the supernatant discarded byaspiration. Assay tubes containing the precipitate were counted for 1min on a LKB1275 gamma counter. Standards and plasma aliquots of thebovine plasma pool were linear (log/logit transformation; r²=0.98) andparallel over a mass of 0.064 to 40 ng/tube and a plasma volume of 25 to300 μL. Total specific binding was 38%, the minimum detectableconcentration was 0.064 ng/tube, percentage recovery of mass was 98.1%,and the inter- and intra-assay CV were 5.2 and 6.8% respectively.

A reduced supply of substrate to the mitochondria could affectmitochondrial respiration rates. Plasma glucose and insulinconcentrations were measured as an indicator of glucose metabolism andsubstrate availability to the mitochondria. Plasma glucose and insulinconcentrations are shown in Table 5.

TABLE 5 Blood parameters of steers with high or low residual feed intake(RFI) Variable Low RFI (n = 9) High RFI (n = 8) Plasma glucose, mg/dL86.44 ± 3.84^(b) 101.12 ± 4.07^(a ) Plasma insulin, ng/mL 9.19 ± 1.0111.10 ± 1.07  Ratio of glucose to insulin 10.04 ± 1.27  10.32 ± 1.35 ^(a,b)Means within a row lacking a common superscript differ (P < 0.05).

High RFI steers were observed to have greater (P<0.05) plasma glucoseconcentrations than low RFI steers. However, plasma insulinconcentrations and the ratio of glucose to insulin did not differbetween the high and low RFI steers. Plasma insulin values are greaterthan those reported in the literature (Yambayamba et al., 1996; Hersomet al., 2004) due to the measurement of plasma insulin values with abovine specific insulin assay. The greater plasma glucose is a result ofthe greater intake of the high RFI steers, however, glucose metabolismdoes not seem to be altered because the ratios of glucose to insulinwere similar between the high and low RFI steers. It appears thatglucose metabolism or availability does not alter mitochondrialrespiration rates.

Example 8 Utilizing Mitochondrial Function in Calculating an ExpectedProgeny Difference Estimate

Expected progeny differences (EPDs) provide estimates of the geneticvalue of an animal as a parent, and have been calculated for bovineanimals (e.g breeds of cattle). Specifically, differences in EPDsbetween two individuals of the same breed predict differences inperformance between their future offspring when each is mated to animalsof the same average genetic merit. EPDs are calculated for birth,growth, maternal, and carcass traits and are reported in the same unitsof measurement as the trait (normally pounds).

EPDs for various traits are reported by most major beef breedassociations, and are calculated using all known information on aparticular animal. This information includes performance data (i.e.,weight records) on the animal itself, information from its ancestors(sire and dam, grandsire, great grandsire, maternal grandsire, etc.),collateral relatives (brothers and sisters), and progeny (includingprogeny that are parents themselves). Measurement of mitochondrialfunction may also be included as a performance parameter in calculatingthe EPD of an animal. These performance records are adjusted for suchfactors as age and sex of the animal, and age of the dam prior toinclusion in EPD databases. These adjustment factors allow performancerecords to be fairly compared in the analysis. Additionally, geneticmerit of mates is accounted in evaluating progeny information.Therefore, progeny records are not influenced by superior or inferiormates. The statistical analysis used for EPD calculation also accountsfor the effects of environment (nutrition, climate, geographicallocation, etc.) that exist between herds. These environmental effectscan be estimated due to the widespread use of artificial insemination(AI). Through AI, the same bull can be used in several herds across thecountry. These common sires create genetic links between herds withdiffering environments and serve as the foundation for evaluation ofperformance data and EPD calculation across herds. For these reasons,animals with published EPDs within a breed may be directly comparedregardless of their age and origin.

All of the methods disclosed and claimed herein can be made and executedwithout undue experimentation in light of the present disclosure. Whilethe compositions and methods of this invention have been described interms of preferred embodiments, it will be apparent to those of skill inthe art that variations may be applied to the methods in the steps or inthe sequence of steps of the methods described herein without departingfrom the concept, spirit and scope of the invention. More specifically,it will be apparent that certain agents which are both chemically andphysiologically related may be substituted for the agents describedherein while the same or similar results would be achieved. All suchsimilar substitutes and modifications apparent to those skilled in theart are deemed to be within the spirit, scope and concept of theinvention as defined by the appended claims.

REFERENCES

The following references, to the extent that they provide exemplaryprocedural or other details supplementary to those set forth herein, arespecifically incorporated herein by reference.

-   U.S. Pat. No. 6,805,075-   U.S. Pat. No. 6,868,804-   WO96/35127-   WO03/032234-   Basarab et al., 2003 Can J. Anim. Sci 83:189-204.-   Bottje et al. 2002; Poultry Sci. 81:546-555.-   Brown, D. R., et al., 1988. J. Anim. Sci. 66:1347-1354.-   Chance et al., 1979. Physiol. Rev. 59:527-605.-   Crews 2005. Gen. Mol. Res. 4:152-165.-   Deleo 1994. Ph.D. dissertation. Curtin University of Technology,    Australia.-   Eastbrook 1967. Meth. Enzymol. 10:41-47.-   Elsasser et al. 1986. Domest. Anim. Endocrinol. 3:277-287.-   Fox et al., 2004. Identifying Differences in Efficiency in Beef    Cattle. Animal Science Department Mimeo 225. Cornell University,    Ithaca, N.Y.-   Hazel, L. N. 1943. Genetics 28:476.-   Herd et al. 2003. J. Anim. Sci. 81:E9-E17.-   Hersom et al., 2004. J. Anim. Sci. 82:2059-2068.-   Iqbal et al., 2004. Poultry Sci. 83:474-484.-   Johnson et al. 2003. J. Anim. Sci. 81:E27-E38.-   Kneeland et al., 2004. J. Anim. Sci. 82:3405-3414.-   Koch et al., 1963. J. Anim. Sci. 22:486-494.-   Lutz and Stahly. 2003. J. Anim. Sci. 81 (Suppl.):141 (Abstr.)-   Moore et al 2005. Aust. J Agr Res, 56:211.-   Nkrumah et al. 2004. J. Anim. Sci. 82: 2451-2459.-   Ojano-Dirain et al., 2004. J Poultry Sci. 83:1394-1403.-   Sandelin et al., 2004. J. Anim. Sci. 82 (Suppl.):416 (Abstr.).-   Sodoyez et al. 1975. J. Biol. Chem. 250:4268-4277.-   USDA, 1997. Official United States Standards for Grading of    Carcasses of Beef. Agric. Marketing. Serv. USDA Washington, D. C.-   Yambayamba et al., 1996. J. Anim. Sci. 74:57-69.

1. A method of breeding livestock based on a desired feed efficiency,comprising the steps of: (a) assaying at least a first candidate head oflivestock for mitochondrial function; (b) correlating the mitochondrialfunction with the mitochondrial function of at least a second head oflivestock having a known feed efficiency to obtain a predicted feedefficiency for the candidate head of livestock; (c) selecting a firstparent head of livestock having a desired predicted feed efficiency; and(d) breeding the first parent head of livestock with a second parenthead of livestock to obtain a progeny head of livestock with anincreased probability of having a desired feed efficiency relative to ahead of livestock of the same breed as said first parent head oflivestock or said second parent head of livestock that has not beenselected for feed efficiency.
 2. The method of claim 1, wherein thefirst candidate head of livestock is a bovine animal.
 3. The method ofclaim 1, wherein the feed efficiency is determined by Residual FeedIntake.
 4. The method of claim 1, wherein the second parent head oflivestock is selected based on mitochondrial function for a desiredpredicted feed efficiency.
 5. The method of claim 4, wherein the secondparent head of livestock is selected by a method comprising the stepsof: (a) assaying a population of livestock for mitochondrial function;(b) correlating the mitochondrial function with the mitochondrialfunction of at least a second head of livestock having a known feedefficiency to obtain a predicted feed efficiency for members of thepopulation; and (c) selecting the second parent head of livestock fromthe population based on said predicted feed efficiency.
 6. The method ofclaim 1, wherein mitochondrial function is determined based on at leastone characteristic selected from the group consisting of oxygenconsumption rate, Complex I electron transport rate, Complex II electrontransport rate, State 2 respiration rate, State 3 respiration rate,Respiratory Control Ratio, and ATP synthesis rate.
 7. The method ofclaim 1, further defined as comprising crossing said progeny head oflivestock with a third head of livestock to produce a second generationprogeny head of livestock.
 8. The method of claim 1, wherein theimproved feed efficiency is a reduced Residual Feed Intake.
 9. Themethod of claim 1, wherein the first parent head of livestock is a headof beef cattle.